feat: implement fast_typing.wdl workflow for #55#75
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Add comprehensive test suite for fast typing workflow (issue #55). Tests verify: - Workflow file structure and location in builtin/ - Import of shared tasks from tasks/ directory - Linear pipeline without alignment stage - Standard inputs (query_sequences, allele_database, profiles_table) - Standardized JSON output format - Strategy metadata (strategy: "fast", alignment_used: false) - MinHash-only allele calling and profile lookup - Edge cases (empty queries, partial profiles) All tests fail as expected (RED phase). Total: 27 failing tests covering file structure, imports, pipeline logic, output format, and execution. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Create torchbase/workflows/builtin/fast_typing.wdl with MinHash-based typing pipeline - Implement shared tasks: minhash.wdl (sketch_sequences, compare_sketches, call_alleles) - Implement profile_lookup.wdl task for profile matching and result generation - Pipeline: sketch query → compare → call alleles → lookup profile - Output includes standardized JSON with method.strategy='fast' and alignment_used=false - Supports multi-scheme torches with scheme-prefixed locus names - All 27 structural and validation tests pass - Syntax validated via miniwdl check Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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- Accept updated profile_lookup.wdl from main - Update fast_typing.wdl to use new output name and alignment_used parameter
- Allow 'alignment_used' parameter in fast workflow (it's metadata, not a task call) - Check specifically for alignment.wdl import, not just presence of word 'alignment' - Check for align_and_call task name, not generic 'align' substring
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Summary
Implements the fast typing strategy workflow that performs allelic typing using MinHash-based similarity only, skipping alignment entirely. This is the fastest strategy suitable for high-quality assemblies or when speed is critical.
fast_typing.wdlworkflow intorchbase/workflows/builtin/minhash.wdlandprofile_lookup.wdlAcceptance Criteria Met
torchbase/workflows/builtin/fast_typing.wdlexistsTest Results
Implementation Details
Co-authored-by: Claude Sonnet 4.5 noreply@anthropic.com